4L7D

Structure of keap1 kelch domain with (1S,2R)-2-{[(1S)-5-methyl-1-[(1-oxo-1,3-dihydro-2H-isoindol-2-yl)methyl]-3,4-dihydroisoquinolin-2(1H)-yl]carbonyl}cyclohexanecarboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Binding Mode and Structure-Activity Relationships around Direct Inhibitors of the Nrf2-Keap1 Complex.

Jnoff, E.Albrecht, C.Barker, J.J.Barker, O.Beaumont, E.Bromidge, S.Brookfield, F.Brooks, M.Bubert, C.Ceska, T.Corden, V.Dawson, G.Duclos, S.Fryatt, T.Genicot, C.Jigorel, E.Kwong, J.Maghames, R.Mushi, I.Pike, R.Sands, Z.A.Smith, M.A.Stimson, C.C.Courade, J.P.

(2014) ChemMedChem 9: 699-705

  • DOI: 10.1002/cmdc.201300525
  • Primary Citation of Related Structures:  
    4L7B, 4L7C, 4L7D, 4N1B

  • PubMed Abstract: 
  • An X-ray crystal structure of Kelch-like ECH-associated protein (Keap1) co-crystallised with (1S,2R)-2-[(1S)-1-[(1,3-dioxo-2,3-dihydro-1H-isoindol-2-yl)methyl]-1,2,3,4-tetrahydroisoquinolin-2-carbonyl]cyclohexane-1-carboxylic acid (compound (S,R,S)-1 a) was obtained ...

    An X-ray crystal structure of Kelch-like ECH-associated protein (Keap1) co-crystallised with (1S,2R)-2-[(1S)-1-[(1,3-dioxo-2,3-dihydro-1H-isoindol-2-yl)methyl]-1,2,3,4-tetrahydroisoquinolin-2-carbonyl]cyclohexane-1-carboxylic acid (compound (S,R,S)-1 a) was obtained. This X-ray crystal structure provides breakthrough experimental evidence for the true binding mode of the hit compound (S,R,S)-1 a, as the ligand orientation was found to differ from that of the initial docking model, which was available at the start of the project. Crystallographic elucidation of this binding mode helped to focus and drive the drug design process more effectively and efficiently.


    Organizational Affiliation

    UCB Pharma, UCB NewMedicines, Chemin du Foriest, 1420 Braine-l'Alleud (Belgium). eric.jnoff@ucb.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kelch-like ECH-associated protein 1A, B, C300Homo sapiensMutation(s): 1 
Gene Names: KEAP1INRF2KIAA0132KLHL19
UniProt & NIH Common Fund Data Resources
Find proteins for Q14145 (Homo sapiens)
Explore Q14145 
Go to UniProtKB:  Q14145
PHAROS:  Q14145
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1VX (Subject of Investigation/LOI)
Query on 1VX

Download Ideal Coordinates CCD File 
D [auth A], G [auth B], K [auth C](1S,2R)-2-{[(1S)-5-methyl-1-[(1-oxo-1,3-dihydro-2H-isoindol-2-yl)methyl]-3,4-dihydroisoquinolin-2(1H)-yl]carbonyl}cyclohexanecarboxylic acid
C27 H30 N2 O4
YTUXAQFRBNUADX-TZRRMPRUSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , H [auth B] , I [auth B] , J [auth B] , L [auth C] , M [auth C] , N [auth C] , 
E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], L [auth C], M [auth C], N [auth C], O [auth C], P [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1VX Binding MOAD:  4L7D IC50: 750 (nM) from 1 assay(s)
BindingDB:  4L7D IC50: 750 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.92α = 90
b = 126β = 90
c = 130.3γ = 90
Software Package:
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 1.1: 2014-04-23
    Changes: Database references